bfactor statistics

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bfactor specifications

Information


Unique identifier OMICS_26901
Name bfactor
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.4
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Nikolaus Grigorieff <>

bfactor in pipelines

 (8)
2017
PMCID: 5736104
PMID: 28682307
DOI: 10.1038/nature23314

[…] procedures and the fsc=0.143 criterion. local resolution was estimated using resmap . the amplitude information of the final maps was corrected by applying a negative b-factor using the program bfactor.exe ., to speed up calculations, the cryo-em data set (871,530 particles) was divided into two halves for the initial round of 3d classification. no symmetry was applied unless otherwise […]

2016
PMCID: 4820614
PMID: 27021073
DOI: 10.1038/ncomms11130

[…] performed applying auto-masking with an initial binarization threshold of 0.008, a binary map extension by 3 pixels and an addition of 5 pixels for soft-edge masking. the map was sharpened with a bfactor of −133 å2 determined by auto-bfactor procedure. the resolution of this trpv2 structure ranges from ∼4.8 å (fsc 0.143) to ∼5.5 å (fsc 0.5). although the overall resolution of the map […]

2016
PMCID: 4935803
PMID: 27380950
DOI: 10.1038/ncomms12026

[…] resolution of 3.6 å (0.143 fsc) and a local resolution extending towards 3.0 å for the core of the 30s and 50s subunits as computed using resmap (). the final maps were subjected to the programme em-bfactor in order to apply an automatically determined negative b-factor for sharpening of the map., initial models for the two ermbl-srcs were obtained by combining: (i) a model of the e. coli 70s […]

2015
PMCID: 4423224
PMID: 25903689
DOI: 10.1038/ncomms7941

[…] the signal recognition particle bound to the ribosome (158,726 particles; 30%), which will be described elsewhere (beckert et al., unpublished). the final volumes were subjected to the program em-bfactor in order to apply an automatically determined negative b-factor for sharpening of the map., the b. subtilis 5s, 16s and 23s rrna sequences were taken from genebank; gene id 2914271, 936774 […]

2015
PMCID: 4605324
PMID: 26384426
DOI: 10.1093/nar/gkv909

[…] (truncation of frequencies higher than 8 å) refinement protocol was used to prevent potential over-fitting (). the final volume was subjected to b-factor sharpening using the program em-bfactor ()., the initial model of human erf1 was based on the crystal structure by cheng et al. () (pdb code: 3e1y-a). the missing minidomain herein was added from the nmr structure of the erf1 c […]


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bfactor in publications

 (53)
PMCID: 5785890
PMID: 29373963
DOI: 10.1186/s12887-018-0991-4

[…] with an individual cronbach’s α coefficient of 0.67. factor ii indicates sports and asthma with an individual cronbach’s α coefficient of 0.75, aquestions of the short form 10-item-questionnaire, bfactor i indicates the use and working mechanism of inhalators and asthma medication with an individual cronbach’s α coefficient of 0.67. factor ii indicates sports and asthma with an individual […]

PMCID: 5706985
PMID: 29021343
DOI: 10.1091/mbc.E17-02-0124

[…] during refinement using a high-resolution noise-substitution test (). using local resolution estimates determined with the blocres program in bsoft, the reconstruction was sharpened with a bfactor of −180 up to a resolution of 5.5 or 4 å for visualization of kinesin or tubulin densities respectively., α1b/βi tubulin was built directly into density in coot () using the recently solved […]

PMCID: 5622526
PMID: 28962549
DOI: 10.1186/s12859-017-1848-9

[…] or the atomic coordinates of the whole protein (for sasa.pdb)., the b factor of the sulfur atom from the methionine of interest extracted from the pdb file used was recorded in the variable bfactor., finally, dpx measures the depth of the sulfur atom from the considered methionine, defined as the distance in ångströms between the s atom and the closest atom from the protein exposed […]

PMCID: 5498776
PMID: 28690376
DOI: 10.6026/97320630013122

[…] in the protein model and is used for making decision about its reliability. errat showed an overall quality factor of 31.544, a result expected for crystallographic models with resolution>2.5a. bfactor analysis is done with what if server reflected the mobility or flexibility of various parts of the molecule. averaged b-factor deviation for protein backbone was 0.082 (z score mean) […]

PMCID: 5450123
PMID: 28558805
DOI: 10.1186/s12955-017-0691-z

[…] possible score and negative self-image (24% of participants had lowest possible score (table ).table 3 aalpha factoring, oblimin rotation on data from the study “living with hiv in sweden” (n = 440) bfactor loadings <-0.32 or >0.32 in bold fig. 2 table 4 aparticipants with complete answers, n = 880 bpossible score for each item 1–4; higher scores reflect a higher level of perceived […]


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